Merge branch '39-add-nf-prov' of https://github.com/ghga-de/nf-platyp…

…usindelcalling into 39-add-nf-prov

CHANGELOG.md

@@ -3,7 +3,36 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v2.0.0 - 28.05.2024
+
+### `Added`
+
+- assets/config/convertToStdVCF.json and bin/convertToStdVCF.py 
+    - Option to output VCF files (all) in standard format (4.2) is added.  Also, TSV formatted confidence annotated/filtrated files are being converted into standard vcf.
+
+- minor changes: 
+    - output names
+### `Fixed`
+
+- Contig processing is only available for hg38 reference. ALT and/or HLA contigs can be given external in a file. 
+    - Automatic generation of HLA/ALT contigs is now possible through tumor BAM instead of fasta.
+
+- conda links in nf-core modules is fixed. 
+    - NOTE: Conda enviroments are not available for the pipeline. Holding conda environment.yml links the same in default creates error even when enable_conda is false.  
+
+- bin/confidenceAnnotation_Indels.py
+    - flag parsing is generic now. 
+    - updated to latest version in https://github.com/DKFZ-ODCF/IndelCallingWorkflow/tree/hg38
+
+- conf/modules.config platypus arguments is fixed (now it is same as dkfz)
+
+### `Dependencies`
+
+### `Deprecated`
+
+- FREQ based filtering is removed from bin/confidenceAnnotation_Indels.py. 
+
+## v1.0dev 
 
 Initial release of nf-core/platypusindelcalling, created with the [nf-core](https://nf-co.re/) template.
 

nextflow.config

@@ -289,6 +289,7 @@ manifest {
 // Nextflow plugins
 plugins {
     id '[email protected]'       // Provenance reports for pipeline runs
+
 }
 
 // Load modules.config for DSL2 module specific options